A polymethine dye is a dye having a linearly conjugated system with an odd number of methine (—CH═) groups, where the terminal heteroatoms N, O, or S, eventually are included in two terminal heterocycles Het1 and Het2. As described herein, polymethines are a delocalized π (pi) electron system, represented by at least in two equivalent formulas shown below:
A monomethine dye has n=0, thus having a single —C═ between the heterocycles. When n=1, the dye is a trimethine, and so on.
Numerous monomethine dyes are known. Some monomethine dyes have the characteristic of no or minimal fluorescence in buffer or in the presence of single stranded DNA (ssDNA) or RNA, but strong fluorescence in the presence of double-stranded DNA (dsDNA). Examples of such dyes, which are commercially useful because of this characteristic, include SYBR Green, Thiazole Orange, BOXTO, Eva Green, and LC Green. SYBR Green, the structure of which is shown below,
is one the most commonly used fluorescent dyes.
Benzopyrylium monomethines are known, but none has the side chain needed for utility in fluorescence studies, and none has been used in dsDNA binding assays.
Other such dyes are desirable.